CSLAP<-read.csv("CSLAP_Dataset_09232019.csv", header=TRUE)
CSLAP$Sample_Year<-as.factor(CSLAP$Sample_Year)
CSLAP$Sample_Month<-as.factor(CSLAP$Sample_Month)
#Split by `Info_Type`
OWCSLAP<-CSLAP[CSLAP$Info_Type == "OW",]
BSCSLAP<-CSLAP[CSLAP$Info_Type == "BS",]
SBCSLAP<-CSLAP[CSLAP$Info_Type == "SB",]
noSBCSLAP<-CSLAP[CSLAP$Info_Type != "SB",]
redCSLAP<-read.csv("redCSLAP.csv")
redOWCSLAP<-redCSLAP[redCSLAP$Info_Type == "OW",]
redBSCSLAP<-redCSLAP[redCSLAP$Info_Type == "BS",]
redSBCSLAP<-redCSLAP[redCSLAP$Info_Type == "SB",]
rednoSBCSLAP<-redCSLAP[redCSLAP$Info_Type != "SB",]
LakeID and Sample_Year#Select out data of interest
df <- OWCSLAP %>% dplyr::select(TP_mg.L, Dreissenids, CA.SA, Mean_Depth_m, Sample_Year, Sample_Month, LakeID)
df <- df[complete.cases(df), ]
#Remove lakes and year 2015
df <- df[df$LakeID != "0601GUI0188",]
df <- df[df$LakeID != "1201ECA0697", ]
df <- df[df$LakeID != "1701LLO0708", ]
df <- df[df$LakeID != "1201GAL0563", ]
df <- df[df$Sample_Year != "2015",]
df$LakeID <- as.factor(as.character(df$LakeID))
OWTP<-lmer(log(TP_mg.L+.01) ~ Dreissenids + log(CA.SA) + Mean_Depth_m + (1|Sample_Year) + (1|Sample_Month) + (1|LakeID) + (1|Sample_Year:LakeID), data=df)
summary(OWTP)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TP_mg.L + 0.01) ~ Dreissenids + log(CA.SA) + Mean_Depth_m +
## (1 | Sample_Year) + (1 | Sample_Month) + (1 | LakeID) + (1 |
## Sample_Year:LakeID)
## Data: df
##
## REML criterion at convergence: -1376.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.4509 -0.5243 -0.1206 0.3339 8.2501
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 3.534e-03 0.059448
## LakeID (Intercept) 2.470e-02 0.157154
## Sample_Month (Intercept) 1.454e-05 0.003813
## Sample_Year (Intercept) 1.275e-03 0.035706
## Residual 2.515e-02 0.158588
## Number of obs: 2114, groups:
## Sample_Year:LakeID, 272; LakeID, 65; Sample_Month, 6; Sample_Year, 5
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -3.767159 0.072209 91.587601 -52.170 < 2e-16 ***
## DreissenidsUninvaded -0.048822 0.046906 174.969528 -1.041 0.299381
## log(CA.SA) 0.017846 0.020804 61.360106 0.858 0.394355
## Mean_Depth_m -0.018813 0.005418 61.964622 -3.472 0.000947 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) DrssnU l(CA.S
## DrssndsUnnv -0.606
## log(CA.SA) -0.584 0.046
## Mean_Dpth_m -0.315 0.004 -0.213
plot(OWTP)
qqmath(OWTP)
qqPlot(resid(OWTP))
## 3989 731
## 1714 272
-Updated 03/08 boundary (singular) fit removed random effect of Sample_Month (variance =0.00), but then output Model failed to converge warning
-Updated 03/09 Model failed to converge fixed by taking log of mean_depth_m and adding only .01 to log(TP_mg.L) instead of 1
BSTP<-lmer(log(TP_mg.L+.01) ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m) + (1|Sample_Month) + (1|LakeID) + (1|Sample_Year:LakeID), data=BSCSLAP)
summary(BSTP)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TP_mg.L + 0.01) ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m) +
## (1 | Sample_Month) + (1 | LakeID) + (1 | Sample_Year:LakeID)
## Data: BSCSLAP
##
## REML criterion at convergence: 3129.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.4705 -0.4411 -0.0672 0.3574 4.9452
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 0.088946 0.2982
## LakeID (Intercept) 0.442456 0.6652
## Sample_Month (Intercept) 0.007073 0.0841
## Residual 0.242080 0.4920
## Number of obs: 1847, groups:
## Sample_Year:LakeID, 275; LakeID, 55; Sample_Month, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -3.04831 0.43720 60.58308 -6.972 2.67e-09 ***
## DreissenidsUninvaded 0.07239 0.20790 140.22374 0.348 0.728
## log(CA.SA) 0.01917 0.09593 51.17992 0.200 0.842
## log(Mean_Depth_m) -0.25814 0.20674 51.50439 -1.249 0.217
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) DrssnU l(CA.S
## DrssndsUnnv -0.427
## log(CA.SA) -0.316 0.093
## lg(Mn_Dpt_) -0.727 -0.031 -0.237
plot(BSTP)
qqPlot(resid(BSTP))
## 3419 20
## 1294 10
Chl<-lmer(log(Extracted_Chl.a_ug.L+1) ~ Dreissenids + log(CA.SA) + Mean_Depth_m + (1|Sample_Year) + (1|Sample_Month) + (1|LakeID) + (1|Sample_Year:LakeID), data=OWCSLAP)
summary(Chl)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(Extracted_Chl.a_ug.L + 1) ~ Dreissenids + log(CA.SA) + Mean_Depth_m +
## (1 | Sample_Year) + (1 | Sample_Month) + (1 | LakeID) + (1 |
## Sample_Year:LakeID)
## Data: OWCSLAP
##
## REML criterion at convergence: 3567.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.1081 -0.5666 -0.0430 0.4943 5.5985
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 0.02531 0.15910
## LakeID (Intercept) 0.08719 0.29527
## Sample_Month (Intercept) 0.01318 0.11481
## Sample_Year (Intercept) 0.00488 0.06986
## Residual 0.19212 0.43831
## Number of obs: 2637, groups:
## Sample_Year:LakeID, 348; LakeID, 69; Sample_Month, 6; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.386082 0.152233 86.432436 9.105 2.89e-14 ***
## DreissenidsUninvaded 0.001903 0.102020 124.230242 0.019 0.9851
## log(CA.SA) 0.052303 0.039062 62.060302 1.339 0.1855
## Mean_Depth_m -0.034230 0.010244 63.502408 -3.341 0.0014 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) DrssnU l(CA.S
## DrssndsUnnv -0.635
## log(CA.SA) -0.533 0.058
## Mean_Dpth_m -0.289 0.013 -0.202
plot(Chl)
qqPlot(resid(Chl))
## 1644 1902
## 810 984
OWTC<-lmer(log(True_Color_PTU) ~ Dreissenids + log(CA.SA) + Mean_Depth_m + (1|Sample_Year) + (1|Sample_Month) + (1|LakeID) + (1|Sample_Year:LakeID), data=OWCSLAP)
summary(OWTC)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(True_Color_PTU) ~ Dreissenids + log(CA.SA) + Mean_Depth_m +
## (1 | Sample_Year) + (1 | Sample_Month) + (1 | LakeID) + (1 |
## Sample_Year:LakeID)
## Data: OWCSLAP
##
## REML criterion at convergence: 2905
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -9.0692 -0.4274 0.0478 0.5218 3.4520
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 0.06706 0.2590
## LakeID (Intercept) 0.18580 0.4310
## Sample_Month (Intercept) 0.01609 0.1269
## Sample_Year (Intercept) 0.07930 0.2816
## Residual 0.13069 0.3615
## Number of obs: 2656, groups:
## Sample_Year:LakeID, 349; LakeID, 69; Sample_Month, 6; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.92827 0.23703 56.49313 8.135 4.36e-11 ***
## DreissenidsUninvaded 0.40617 0.14164 146.82212 2.868 0.00474 **
## log(CA.SA) 0.17743 0.05636 64.59212 3.148 0.00249 **
## Mean_Depth_m -0.03653 0.01476 65.70210 -2.475 0.01592 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) DrssnU l(CA.S
## DrssndsUnnv -0.566
## log(CA.SA) -0.491 0.055
## Mean_Dpth_m -0.266 0.011 -0.202
plot(OWTC)
qqPlot(resid(OWTC))
## 3893 1323
## 2050 647
OWTN<-lmer(log(TN_mg.L+1) ~ Dreissenids + log(CA.SA) + Mean_Depth_m + (1|Sample_Year) + (1|Sample_Month) + (1|LakeID) + (1|Sample_Year:LakeID), data=OWCSLAP)
summary(OWTN)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TN_mg.L + 1) ~ Dreissenids + log(CA.SA) + Mean_Depth_m +
## (1 | Sample_Year) + (1 | Sample_Month) + (1 | LakeID) + (1 |
## Sample_Year:LakeID)
## Data: OWCSLAP
##
## REML criterion at convergence: -2875.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.5181 -0.4198 -0.0970 0.2786 16.7221
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 1.662e-03 0.040762
## LakeID (Intercept) 8.564e-03 0.092542
## Sample_Month (Intercept) 1.772e-05 0.004209
## Sample_Year (Intercept) 6.207e-04 0.024914
## Residual 1.728e-02 0.131454
## Number of obs: 2685, groups:
## Sample_Year:LakeID, 351; LakeID, 69; Sample_Month, 6; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.353394 0.044515 94.196359 7.939 4.24e-12 ***
## DreissenidsUninvaded -0.068006 0.030759 142.438616 -2.211 0.0286 *
## log(CA.SA) 0.023022 0.012101 65.399059 1.902 0.0615 .
## Mean_Depth_m -0.004547 0.003167 66.369319 -1.436 0.1557
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) DrssnU l(CA.S
## DrssndsUnnv -0.656
## log(CA.SA) -0.564 0.059
## Mean_Dpth_m -0.304 0.012 -0.203
plot(OWTN)
qqPlot(resid(OWTN))
## 4237 271
## 2294 141
-Update 03/08 Model failed to converge removed log-transformation of Secchi to resolve
Secchi<-lmer(Secchi_Depth_m ~ Dreissenids + log(CA.SA) + Mean_Depth_m + (1|Sample_Year) + (1|Sample_Month) + (1|LakeID) + (1|Sample_Year:LakeID), data=noSBCSLAP)
summary(Secchi)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Secchi_Depth_m ~ Dreissenids + log(CA.SA) + Mean_Depth_m + (1 |
## Sample_Year) + (1 | Sample_Month) + (1 | LakeID) + (1 | Sample_Year:LakeID)
## Data: noSBCSLAP
##
## REML criterion at convergence: 7132.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.3068 -0.5516 -0.0576 0.4900 8.6962
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 0.185273 0.43043
## LakeID (Intercept) 1.404778 1.18523
## Sample_Month (Intercept) 0.002397 0.04896
## Sample_Year (Intercept) 0.017177 0.13106
## Residual 0.691860 0.83178
## Number of obs: 2636, groups:
## Sample_Year:LakeID, 348; LakeID, 69; Sample_Month, 6; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.44908 0.50427 102.67491 8.823 3.10e-14 ***
## DreissenidsUninvaded -0.49818 0.31798 242.91686 -1.567 0.11849
## log(CA.SA) -0.43879 0.15132 65.67386 -2.900 0.00507 **
## Mean_Depth_m 0.17773 0.03954 66.13573 4.496 2.87e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) DrssnU l(CA.S
## DrssndsUnnv -0.597
## log(CA.SA) -0.610 0.047
## Mean_Dpth_m -0.334 0.009 -0.201
plot(Secchi)
qqPlot(resid(Secchi))
## 4432 4814
## 2362 2553
-update 03/08 boundary (singular) fit Removed random effect of Sample_Year with ~0.00 variance to resolve warning.
SBChl<-lmer(log(ESF_Chl.a_ug.L) ~ Dreissenids + log(CA.SA) + Mean_Depth_m + (1|Sample_Month) + (1|LakeID) , data=SBCSLAP)
summary(SBChl)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(ESF_Chl.a_ug.L) ~ Dreissenids + log(CA.SA) + Mean_Depth_m +
## (1 | Sample_Month) + (1 | LakeID)
## Data: SBCSLAP
##
## REML criterion at convergence: 1009.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.92271 -0.59622 0.08345 0.64958 2.26019
##
## Random effects:
## Groups Name Variance Std.Dev.
## LakeID (Intercept) 2.1628 1.4707
## Sample_Month (Intercept) 0.1258 0.3546
## Residual 4.3414 2.0836
## Number of obs: 224, groups: LakeID, 43; Sample_Month, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.1636 1.3187 30.0632 4.674 5.81e-05 ***
## DreissenidsUninvaded -0.9296 0.8286 32.5716 -1.122 0.270
## log(CA.SA) 0.3225 0.3291 37.9537 0.980 0.333
## Mean_Depth_m -0.1267 0.1183 33.4354 -1.071 0.292
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) DrssnU l(CA.S
## DrssndsUnnv -0.665
## log(CA.SA) -0.589 0.115
## Mean_Dpth_m -0.546 0.120 0.003
plot(SBChl)
qqPlot(resid(SBChl))
## 1490 1096
## 110 66
-update 03/08 boundary (singular) fit Removed random effect of Sample_Month with 0.00 variance to resolve warning.
SBmicro<-lmer(log(ESF_Microcystin_ug.L) ~ Dreissenids + log(CA.SA) + Mean_Depth_m + (1|Sample_Year) + (1|LakeID) + (1|Sample_Year:LakeID), data=SBCSLAP)
summary(SBmicro)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(ESF_Microcystin_ug.L) ~ Dreissenids + log(CA.SA) + Mean_Depth_m +
## (1 | Sample_Year) + (1 | LakeID) + (1 | Sample_Year:LakeID)
## Data: SBCSLAP
##
## REML criterion at convergence: 180.6
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.34775 -0.55174 0.05929 0.61275 1.78337
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 1.366 1.169
## LakeID (Intercept) 1.174 1.084
## Sample_Year (Intercept) 1.584 1.259
## Residual 2.217 1.489
## Number of obs: 46, groups: Sample_Year:LakeID, 16; LakeID, 7; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 7.3562 4.4643 1.2249 1.648 0.312
## DreissenidsUninvaded 0.4430 1.7074 0.6926 0.259 0.851
## log(CA.SA) -0.9760 2.0096 1.5301 -0.486 0.688
## Mean_Depth_m -0.3968 0.3945 2.1521 -1.006 0.414
##
## Correlation of Fixed Effects:
## (Intr) DrssnU l(CA.S
## DrssndsUnnv 0.311
## log(CA.SA) -0.896 -0.574
## Mean_Dpth_m -0.725 -0.187 0.468
plot(SBmicro)
qqPlot(resid(SBmicro))
## 1088 1100
## 26 32
-update 03/08 Model failed to converge. Removed random effect of LakeID to ~0.00 variance to resolve warning.
redOWTP<-lmer(log(TP_mg.L+1) ~ Dreissenids.x + (1|Sample_Year) + (1|Sample_Month) + (1|Sample_Year:LakeID), data=redOWCSLAP)
summary(redOWTP)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(TP_mg.L + 1) ~ Dreissenids.x + (1 | Sample_Year) + (1 | Sample_Month) +
## (1 | Sample_Year:LakeID)
## Data: redOWCSLAP
##
## REML criterion at convergence: -4537
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.8575 -0.3194 -0.0984 0.1809 9.2298
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 2.546e-05 0.0050460
## Sample_Month (Intercept) 3.774e-06 0.0019427
## Sample_Year (Intercept) 6.987e-07 0.0008359
## Residual 3.346e-05 0.0057840
## Number of obs: 633, groups:
## Sample_Year:LakeID, 80; Sample_Month, 6; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.013652 0.001268 7.336205 10.770 9.31e-06 ***
## Dreissenids.xUninvaded -0.001673 0.001223 72.882134 -1.368 0.176
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## Drssnds.xUn -0.499
plot(redOWTP)
qqPlot(resid(redOWTP))
## 717 155
## 343 72
-Update 03/08 boundary (singular) fit removed random effect of LakeID (variance = 0.00) to resolve warning -Update 05/15* boundary (singular) fit removed random effect of Sample Year to resolve warning
redBSTP<-lmer(log(TP_mg.L+1) ~ Dreissenids.x + (1|Sample_Month) + (1|Sample_Year:LakeID), data=redBSCSLAP)
summary(redBSTP)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TP_mg.L + 1) ~ Dreissenids.x + (1 | Sample_Month) + (1 |
## Sample_Year:LakeID)
## Data: redBSCSLAP
##
## REML criterion at convergence: -1577.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.2990 -0.3892 -0.1515 0.1008 5.9510
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 0.0010249 0.03201
## Sample_Month (Intercept) 0.0001643 0.01282
## Residual 0.0014448 0.03801
## Number of obs: 465, groups: Sample_Year:LakeID, 70; Sample_Month, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.113e-02 8.026e-03 7.482e+00 5.125 0.00111 **
## Dreissenids.xUninvaded 3.148e-05 8.594e-03 6.688e+01 0.004 0.99709
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## Drssnds.xUn -0.458
plot(redBSTP)
qqPlot(resid(redBSTP))
## 582 600
## 222 229
-Update 03/10 Model failed to converge fixed by adding .01 to log(Extracted_Chl.a_ug.L) instead of 1
redChl<-lmer(log(Extracted_Chl.a_ug.L+.01) ~ Dreissenids.x + (1|Sample_Year) + (1|Sample_Month) + (1|LakeID) + (1|Sample_Year:LakeID), data=redOWCSLAP)
summary(redChl)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log(Extracted_Chl.a_ug.L + 0.01) ~ Dreissenids.x + (1 | Sample_Year) +
## (1 | Sample_Month) + (1 | LakeID) + (1 | Sample_Year:LakeID)
## Data: redOWCSLAP
##
## REML criterion at convergence: 1311.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.0084 -0.4983 0.0557 0.5255 4.4665
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 0.07208 0.2685
## LakeID (Intercept) 0.06533 0.2556
## Sample_Month (Intercept) 0.02666 0.1633
## Sample_Year (Intercept) 0.01453 0.1205
## Residual 0.41063 0.6408
## Number of obs: 619, groups:
## Sample_Year:LakeID, 81; LakeID, 16; Sample_Month, 6; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.75642 0.13640 16.46580 5.546 3.99e-05 ***
## Dreissenids.xUninvaded -0.03641 0.13878 16.81418 -0.262 0.796
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## Drssnds.xUn -0.529
plot(redChl)
qqPlot(resid(redChl))
## 739 705
## 353 323
Update 03/31 Removed Sample_Month:LakeID to alleviate Convergence Code error
redOWTC<-lmer(log(True_Color_PTU) ~ Dreissenids.x + (1|Sample_Year) + (1|Sample_Month) + (1|LakeID) + (1|Sample_Year:LakeID), data=redOWCSLAP)
summary(redOWTC)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(True_Color_PTU) ~ Dreissenids.x + (1 | Sample_Year) + (1 |
## Sample_Month) + (1 | LakeID) + (1 | Sample_Year:LakeID)
## Data: redOWCSLAP
##
## REML criterion at convergence: 776.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.2627 -0.3668 0.0747 0.4767 2.6381
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 0.08615 0.2935
## LakeID (Intercept) 0.04597 0.2144
## Sample_Month (Intercept) 0.01141 0.1068
## Sample_Year (Intercept) 0.12121 0.3481
## Residual 0.15246 0.3905
## Number of obs: 623, groups:
## Sample_Year:LakeID, 81; LakeID, 16; Sample_Month, 6; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 2.2630 0.1751 9.6432 12.924 2.09e-07 ***
## Dreissenids.xUninvaded 0.4237 0.1215 22.0556 3.488 0.00208 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## Drssnds.xUn -0.360
plot(redOWTC)
qqPlot(resid(redOWTC))
## 1075 381
## 534 169
-Update 03/10 Model failed to converge resolved by removing low variance factor of Sample_Month and adding .01 to log(TN_mg.L) instead of 1.0 -Update 05/15 Model failed to converge resolved by adding 1.0 to log(TN_mg.L) instead of 0.1
redOWTN<-lmer(log(TN_mg.L+1) ~ Dreissenids.x + (1|Sample_Year) + (1|LakeID) + (1|Sample_Year:LakeID), data=redOWCSLAP)
summary(redOWTN)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(TN_mg.L + 1) ~ Dreissenids.x + (1 | Sample_Year) + (1 | LakeID) +
## (1 | Sample_Year:LakeID)
## Data: redOWCSLAP
##
## REML criterion at convergence: -820.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.7948 -0.4689 -0.0987 0.3629 10.6434
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 0.0029898 0.05468
## LakeID (Intercept) 0.0210664 0.14514
## Sample_Year (Intercept) 0.0007878 0.02807
## Residual 0.0124601 0.11162
## Number of obs: 626, groups: Sample_Year:LakeID, 81; LakeID, 16; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.37732 0.04576 24.10267 8.246 1.78e-08 ***
## Dreissenids.xUninvaded -0.05624 0.04641 68.00433 -1.212 0.23
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## Drssnds.xUn -0.529
plot(redOWTN)
qqPlot(resid(redOWTN))
## 592 884
## 268 434
Update 05/15 boundary (singular) fit resolved by removing Sample Month (variance = 0.00) Update 05/15 Model failed to converge resolved by NOT log transforming Secchi depth
redSecchi<-lmer(Secchi_Depth_m ~ Dreissenids.x + (1|Sample_Year) + (1|LakeID) + (1|Sample_Year:LakeID), data=rednoSBCSLAP)
summary(redSecchi)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Secchi_Depth_m ~ Dreissenids.x + (1 | Sample_Year) + (1 | LakeID) +
## (1 | Sample_Year:LakeID)
## Data: rednoSBCSLAP
##
## REML criterion at convergence: 1732
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.7937 -0.5728 -0.1050 0.4748 4.6028
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year:LakeID (Intercept) 0.33613 0.5798
## LakeID (Intercept) 0.79888 0.8938
## Sample_Year (Intercept) 0.02658 0.1630
## Residual 0.73189 0.8555
## Number of obs: 622, groups: Sample_Year:LakeID, 81; LakeID, 16; Sample_Year, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.4327 0.3097 21.6218 14.314 1.66e-12 ***
## Dreissenids.xUninvaded -0.6381 0.3638 41.5168 -1.754 0.0868 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## Drssnds.xUn -0.613
plot(redSecchi)
qqPlot(resid(redSecchi))
## 1131 86
## 557 33
-update 03/08 boundary (singular) fit removed random effect of Sample_Year and Sample_Year:LakeID to resolve
redSBChl<-lmer(log(ESF_Chl.a_ug.L) ~ Dreissenids.x + (1|Sample_Month) + (1|LakeID), data=redSBCSLAP)
summary(redSBChl)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(ESF_Chl.a_ug.L) ~ Dreissenids.x + (1 | Sample_Month) + (1 |
## LakeID)
## Data: redSBCSLAP
##
## REML criterion at convergence: 487
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.78776 -0.50698 0.02912 0.62718 2.18332
##
## Random effects:
## Groups Name Variance Std.Dev.
## LakeID (Intercept) 2.8606 1.6913
## Sample_Month (Intercept) 0.3031 0.5505
## Residual 4.2716 2.0668
## Number of obs: 110, groups: LakeID, 9; Sample_Month, 6
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.4371 0.8905 10.9537 7.229 1.73e-05 ***
## Dreissenids.xUninvaded -0.8028 1.1077 15.4213 -0.725 0.479
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## Drssnds.xUn -0.633
plot(redSBChl)
qqPlot(resid(redSBChl))
## 511 319
## 75 46
-Update 03/08 boundary (singular) fit, model matrix error, and model failed to converge so removed random effect of Sample_Year:LakeID, random effect of month, and fixed effect of Mean_Depth_m to resolve
redMicro<-lmer(log(ESF_Microcystin_ug.L+1) ~ Dreissenids.x + (1|Sample_Year) + (1|LakeID), data=redSBCSLAP)
summary(redMicro)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log(ESF_Microcystin_ug.L + 1) ~ Dreissenids.x + (1 | Sample_Year) +
## (1 | LakeID)
## Data: redSBCSLAP
##
## REML criterion at convergence: 145.8
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.2729 -0.6885 0.2355 0.6176 1.9123
##
## Random effects:
## Groups Name Variance Std.Dev.
## Sample_Year (Intercept) 3.3346 1.8261
## LakeID (Intercept) 0.2482 0.4982
## Residual 2.1777 1.4757
## Number of obs: 38, groups: Sample_Year, 5; LakeID, 3
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.18486 1.00872 0.69435 4.149 0.230
## Dreissenids.xUninvaded 0.60562 0.85431 0.07754 0.709 0.881
##
## Correlation of Fixed Effects:
## (Intr)
## Drssnds.xUn -0.406
plot(redMicro)
qqPlot(resid(redMicro))
## 264 282
## 21 25